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Open Access Technical Note

RCDI/eRCDI: a web-server to estimate codon usage deoptimization

Pere Puigbò1*, Lluís Aragonès2 and Santiago Garcia-Vallvé3

Author Affiliations

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

2 Department of Microbiology, University of Barcelona, 08028 Barcelona, Spain

3 Department of Biochemistry and Biotechnology, Nutrigenomics Research Group, Rovira i Virgili University, 43007 Tarragona, Spain

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BMC Research Notes 2010, 3:87  doi:10.1186/1756-0500-3-87

Published: 31 March 2010

Abstract

Background

The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome.

Findings

RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at http://genomes.urv.cat/CAIcal/RCDI webcite.

Conclusions

This web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression.